Chun Liang


350 Pearson Hall  (513) 529-2336

Biographical Information

My bioinformatics lab focuses on three primary research areas: (1) develop bioinformatics software tools, (2) build and maintain biological databases, and (3) conduct data analysis and data mining to address interesting biological questions.  Currently, we are working with many different bioinformatics projects, including genome-wide detection and functional characterization of DNA and RNA transposons, In silico exploration of DNA repeats (e.g., inverted repeats) and their potential roles in gene expression regulation, CRISPR-based DNA and RNA editing: target design and specificity, genome-wide detection of CRISPRs in prokaryotic genomes, DNA methylation and its role in tissue regeneration, RNA-Seq based transcriptome analysis and differentially expressed gene analysis, small non-coding RNAs (miRNAs, siRNAs and piRNAs) biogenesis and their differential expression analysis, genome-wide analysis of alternative polyadenylation and alternative splicing in eukaryotes, etc.

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Courses Taught

BIO/CHM/CSE/MBI 466-566: Bioinformatics Computing Skills
BIO/MBI 485-585 CSE 456-556: Bioinformatics Principles
BIO/CSE/MBI 256: Introduction to Programming for the Life Sciences
BIO 131: Plants, Humanity, and the Environment 

Publications (2004-2017)
 (*Corresponding Author; **Co-Corresponding Author; +Undergraduate Student; ++Graduate Student)

Moller AG++, Liang C* (2017) MetaCRAST: reference-guided extraction of CRISPR spacers from unassembled metagenomes. PeerJ, 5:e3788

Shi J++, Li X, Dong M, Graham M+, Yadav N+, Liang C* (2017) JNSViewer - a JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures. PLOS ONE, 12(6):e0179040

Guo C++, Spinelli M+, Ye C, Li QQ**, Liang C**(2017) Genome-Wide Comparative Analysis of Miniature Inverted Repeat Transposable Elements in 19 Arabidopsis thaliana Ecotype Accessions. Scientific Reports, 7:2634

Wang K++, Liang C* (2017) CRF: detection of CRISPR arrays using random forest. PeerJ, 5:e3219

Raj-Kumar P++**, Vallon O, Liang C** (2017) In silico analysis of the sequence features responsible for alternatively spliced introns in the model green alga Chlamydomonas reinhardtii. Plant Mol Biol, 94:253-265

Moller AG++, Liang C* (2017) Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics. PeerJ, 5:e2844.

Guo C++, Spinelli M+, Liu M, Li QQ**, Liang C** (2016) A Genome-wide Study of "Non-3UTR" Polyadenylation Sites in Arabidopsis thaliana, Scientific Reports, 6:28060.

Li L, Guo C++, Wang B, Zhou T, Lei Y, Dai Y, He W, Liang C**, Wang X** (2016) RNAi-mediated transgenic rice resistance to Rice stripe virus, Journal of Integrative Agriculture, 15:60345-7.

Zhu H++, Misel L+, Graham M+, Robinson ML, Liang C* (2016) CT-Finder: A Web Service for CRISPR Optimal Target Prediction and Visualization, Scientific Reports, 6:25516.

Ye C++, Ji G, Liang C* (2016) detectMITE: A novel approach to detect miniature inverted repeat transposable elements in genomes, Scientific Reports, 6:19688.

Shi J++, Dong M++, Li L++, Liu L, Luz-Madrigal A, Tsonis PA, Rio-Tsonis KD, Liang C* (2015) mirPRo - a novel standalone program for differential expression and variation analysis of miRNAs, Scientific Reports, 5:14617.

Kumar PK++, Hoang TV++, Robinson ML, Tsonis PA, Liang C* (2015) CADBURE: A generic tool to evaluate the performance of spliced aligners on RNA-Seq data, Scientific Reports, 5:13443.

Li L++, Ji G, Ye C++, Shu C, Zhang J, Liang C** (2015) PlantOrDB: a genome-wide ortholog database for land plants and green algae, BMC Plant Biology, 15:161.

Guo C++, Li L, Wang X, Liang C** (2015) Alterations in siRNA and miRNA expression profiles detected by deep sequencing of transgenic rice with siRNA-mediated viral resistance, PLOS ONE, 10(1):e0116175.

Dong M++, Ji G, Li QQ, Liang C* (2015) Extraction of Poly(A) Sites from Large-Scale RNA-seq Data, Methods Mol Biol, 1255:25-37.

Wang K++, Liang C, Liu J, Xiao H, Huang S, Xu J, Li F (2014) Prediction of piRNAs using transposon interaction and a support vector machine. BMC Bioinformatics, 15:6593.

Ye C++, Ji G, Li L++, Liang C** (2014) detectIR: a novel program for detecting perfect and imperfect inverted repeats using complex numbers and vector calculation, PLOS ONE, 9(11):e0113349.

Geng L, Duan X, Liang C, Shu C, Song F, Zhang J (2014) Mining tissue-specific contigs from peanut for promoter cloning by deep transcriptome sequencing, Plant Cell Physiol, 55:1793-1801.

Hoang TV++, Raj Kumar PK++, Sreeskandarajan S++, Tsonis PA, Liang C, Robinson M (2014) Comparative transcriptome analysis of epithelial and fiber cells in newborn mouse lenses by RNA sequencing, Molecular Vision, 20:1491-1517.

Mao R++, Kumar PR++, Guo C++, Zhang Y, Liang C** (2014) Comparative analyses between retained introns and constitutively spliced introns in Arabidopsis thaliana using random forest and support vector machine, PLOS ONE, 9(8):e104049.

Morton TJ+, Abrudan P+, Figueroa N, Liang C**, Karro JE (2014) SCOPE++: Sequence Classification Of homoPolymer Emissions, Genomics, 104:157-162

Batesole K+, Wimalanathan K++, Liu L, Echt CS, Zhang F+, Liang C* (2014) YouGenMap: A web platform for dynamic multi-comparative mapping and visualization of genetic maps. Frontiers in Genetics, 5:183.

Ray WC, Wolock SL, Callahan NW, Dong M++, Li QQ, Liang C, Magliery T, Bartlett CW (2014) Addressing the unmet need for visualizing conditional random fields in biological data. BMC Bioinformatics, 15:202.

Sreeskandarajan S++, Flowers MM, Karro J, Liang C** (2014) A MATLAB-based tool for accurate detection of perfect overlapping and nested inverted repeats in DNA sequences. Bioinformatics, 30:887-8.

Zhao Z++, Guo C++, Sutharzan S++, Li P++, Echt CS, Zhang J, Liang C* (2014) Genome-wide analysis of tandem repeats in plants and green algae. G3: Genes, Genomics and Genetics, 4:67-78.

Zhao Z++, Wu X, Kumar PK++, Dong M++, Ji G, Li QQ, Liang C** (2014) Bioinformatics analysis of alternative polyadenylation in green alga Chlamydomonas reinhardtii using transcriptome sequences from three different sequencing platforms. G3: Genes, Genomics and Genetics, 4:871-83.

Ream DC, Murakami ST, Schmidt E+, Huang GH, Liang C, Friedberg I, Cheng XW (2013). Comparative analysis of error-prone replication mononucleotide repeats across baculovirus genomes. Virus Res, 178(2):217-225.

Li P++, Ji G, Dong M++, Schmidt E+, Lenox D+, Chen L++, Liu Q++, Liu L, Zhang J and Liang C** (2012) CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis. Bioinformatics, 28(18):2382-2384.

Duan X++, Schmidt E+, Li P++, Lenox D+, Liu L, Shu C, Zhang J and Liang C** (2012) PeanutDB: An integrated bioinformatics web portal for Arachis hypogaea transcriptomics. BMC Plant Biology, 12:94.

Sun Zhou, Guoli Ji, Xiaolin Liu, Li P++, Moler J, Karro JE and Liang C** (2012) Pattern analysis approach reveals restriction enzyme cutting abnormalities and other cDNA library construction artifacts using raw EST data. BMC Biotechnology, 12:16.

Gong P, Guan X, Pirooznia M, Liang C, and Perkins EJ. (2012) Gene Expression Analysis of CL-20-Induced Reversible Neurotoxicity Reveals GABA(A) Receptors as Potential Targets in the Earthworm Eisenia fetida. Environ Sci Technol, 46(2):1223-32.

Wu X, Liu M, Downie B, Liang C, Ji G, Li QQ and Hunt AG (2011) Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation. PNAS, 108(30):12533-12538.

Specht M, Stanke M, Terashima M, Naumann-Busch B, Janssen I, Hohner R, Hom EFY, Liang C and Hippler M (2011) Concerted action of the new Genomic Peptide Finder and AUGUSTUS allows for automated proteogenomic annotation of the Chlamydomonas reinhardtii genome. Proteomics, 11(9):1814-1823.

Echt CS, Saha S, Krutovsky KV, Wimalanathan K++, Erpelding JE, Liang C and CD Nelson (2011) An annotated genetic map of loblolly pine based on microsatellite and cDNA markers. BMC Genetics, 12:17.

Rao DM, Moler JC++, Ozden M, Zhang Y++, Liang C** and JE Karro (2010) PEACE: Parallel Environment for Assembly and Clustering of Gene Expression. Nucleic Acids Research, 38:W737-W742.

Liang C*, Liu L and G Ji (2009) WebGMAP: a web service for mapping and aligning cDNA sequences to genomes. Nucleic Acids Research, 37:W77-W83.

Liang C*, Liu Y++, Liu L, Davis AC+, Shen Y++ and QQ Li (2008) ESTs with cDNA termini - previously overlooked resources for gene annotation and transcriptome exploration in Chlamydomonas reinhardtii. Genetics, 179:83-93.

Shen Y++, Liu Y++, Liu L, Liang C and QQ Li (2008) Unique features of nuclear mRNA poly(A) signals and alternative polyadenylation in Chlamydomonas reinhardtii. Genetics, 179:167-176.

Conner JA, Goel S, Gunawan G, Cordonnier-Pratt M-M, Johnson VE, Liang C, Wang H, Pratt LH, Mullet JE, DeBarry J, Yang L, Bennetzen JL, Klein PE, and P Ozias-Akins (2008) Sequence Analysis of Bacterial Artificial Chromosome Clones from the Apospory-Specific Genomic Region of Pennisetum and Cenchrus. Plant Physiology, 147: 1396-1411.

Liang C*, Wang G, Liu L, Ji G, Fang L, Liu Y++, Carter K+, Webb JS+ and JFD Dean (2007) ConiferEST: an integrated bioinformatics system for data reprocessing and mining of conifer expressed sequence tags (ESTs). BMC Genomics, 8:134.

Liang C*, Wang G, Liu L, Ji G, Liu Y++, Chen J++, Webb JS+, Reese G, and JFD Dean (2007) WebTraceMiner: a web service for processing and mining EST sequence trace files. Nucleic Acids Research, 35:W137-W142.

Liang C, Sun F, Wang H, Qu J, Freeman RM Jr, Pratt LH, M-M Cordonnier-Pratt (2006) MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools. BMC Bioinformatics, 7:115.

Lorenz WW, Sun F, Liang C, Kolychev DS, Wang H, Zhao X, Cordonnier-Pratt M-M, Pratt LH, and JFD Dean (2006) Water stress-responsive genes in loblolly pine (Pinus taeda) roots identified by analysis of expressed sequence tag libraries. Tree Physiology, 26:1-16.

Pratt LH, Liang C, Shah M, Sun F, Wang H, Reid SP, Gingle AR, Paterson AH, Wing R, Dean R, Klein R, Nguyen HT, Ma H-M, Zhao X, Morishige DT, Mullet JE, and M-M Cordonnier-Pratt (2005) Sorghum Expressed Sequence Tags Identify Signature Genes for Drought, Pathogenesis and Skotomorphogenesis from a Milestone Set of 16,801 Unique Transcripts. Plant Physiology, 139:869-884.